Centromeric Alpha Repeat Monomer Array Length Estimator
Estimate alpha-repeat length from independently observed copies and monomer length; no assumed exact universal 171-bp composition.
Description
Estimate alpha-repeat length from independently observed copies and monomer length; no assumed exact universal 171-bp composition.
A repeat-array length estimate can multiply observed copy count by a declared monomer size. The estimate is conditional on treating those repeats as uniform contiguous copies.
When to use this tool
Estimate alpha-repeat length from independently observed copies and monomer length; no assumed exact universal 171-bp composition.
- Prepare the supplied observedMonomerCopies, callerMonomerLengthBp fields for this operation.
- Compare the complete example with the representation used by your own input before carrying the result into another step.
How to use the tool and how it works
- Enter observedMonomerCopies, callerMonomerLengthBp. Use the exact text syntax, units and index conventions explained below.
- Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
- Read result.conditionalArrayLengthBp, result.gapsOrSequenceVariationIncluded. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Validate a nonnegative integer observedMonomerCopies and positive bounded callerMonomerLengthBp. Multiply them to return conditionalArrayLengthBp and set gapsOrSequenceVariationIncluded false.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| observedMonomerCopies | observed monomer copies. | Integer from 0 to 1e9 inclusive |
| callerMonomerLengthBp | caller monomer length bp. | Integer from 1 to 10000 inclusive |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.conditionalArrayLengthBp | The conditional array length bp value under the stated formula or text convention. |
| result.gapsOrSequenceVariationIncluded | Flag for gaps or sequence variation included under the exact condition described above. |
{
"input": {
"observedMonomerCopies": 10,
"callerMonomerLengthBp": 171
},
"output": {
"result": {
"conditionalArrayLengthBp": 1710,
"gapsOrSequenceVariationIncluded": false
}
}
}Limitations and assumptions
- No repeat annotation, assembly inspection or centromere boundary detection is performed. Gaps, partial copies and varying monomer lengths are excluded from the model.
- Every declared top-level field is required and unexpected fields are rejected. Numeric inputs must be finite; ordinary text fields are bounded to 8,192 UTF-16 code units, with tighter operation-specific limits where stated.
- Ordinary string lists have at most 128 entries of at most 128 code units each; numeric lists and matrices have separate bounded size checks. Nonfinite results and excessively large serialized outputs are rejected.
- Indexes are zero-based and spans have an exclusive end unless explicitly stated otherwise. A valid false, null or empty-list result is distinct from malformed input.
Alternative or Complementary methods
Retain the reference assembly, accession/version and measurement convention with an analysis. Length summaries, flags and lookup notes do not validate an assembly or classify a variant; use the corresponding sequence, alignment or evidence-review workflow.
References
Similar or alternative tools
- inverted repeat scan
An inverted repeat contains DNA arms that are reverse complements separated by a spacer.
- tandem repeat copy number
A tandem repeat consists of adjacent exact motif copies.